Reconstruction of metabolic networks from genome data and analysis 
of their global structure for various organisms

Ma, Hongwu; Zeng, An

doi:10.1093/bioinformatics/19.2.270

Cited by 435 publications

(468 citation statements)

References 24 publications

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“…Using the new technique, we found evidence supporting the view that organisms that evolve in more uncertain environments exhibit more complex metabolic connectivity structures than those evolving under more stable conditions. Note, that the motif based approach forwarded here strongly supports the view that environmental conditions play a pivotal role in shaping the resultant metabolic networks, and is robust in the sense that the patterns described in Figures 2 and 3 are reproducible in both the latest and older, less complete versions of the data 42 (data not shown). This is in contrast to recent studies in which network features that were found to correlate with environmental variability (e.g.…”

Section: Discussionsupporting

confidence: 70%

Network motif frequency vectors reveal evolving metabolic network organisation

2015

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At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over the past decade or so. Such investigations have revealed a number of shared topological features, such as a short characteristic path-length, large clustering coefficient and hierarchical modular structure. However, the extent to which evolutionary and functional properties of metabolism manifest via this underlying network architecture remains unclear. In this paper, we employ a novel graph embedding technique, based upon low-order network motifs, to compare metabolic network structure for 383 bacterial species categorised according to a number of biological features. In particular, we introduce a new global significance score which enables us to quantify important evolutionary relationships that exist between organisms and their physical environments. Using this new approach, we demonstrate a number of significant correlations between environmental factors, such as growth conditions and habitat variability, and network motif structure, providing evidence that organism adaptability leads to increased complexities in the resultant metabolic networks.

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Section: Discussionsupporting

confidence: 70%

Network motif frequency vectors reveal evolving metabolic network organisation

2015

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“…4 and SI Fig. 13): the KEGG database (40,41), the Ma-Zeng database (42), and the reconstruction compiled by Palsson's Systems Biology Laboratory at the UCSD (43). In these networks, nodes are metabolites and two metabolites are connected if there is a reaction that transforms one into the other (44).…”

Section: Application To Metabolic Networkmentioning

confidence: 99%

Extracting the hierarchical organization of complex systems

Sales‐Pardo

Guimerà²,

Moreira³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

493

363

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Extracting understanding from the growing ``sea'' of biological and socio-economic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method that is able to accurately extract the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs, which we use to validate the method. We then apply our method to real-world networks, including the air-transportation network, an electronic circuit, an email exchange network, and metabolic networks. We find that our method enables us to obtain an accurate multi-scale descriptions of a complex system.Comment: Figures in screen resolution. Version with full resolution figures available at http://amaral.chem-eng.northwestern.edu/Publications/Papers/sales-pardo-2007.pd

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“…(a) Topological consistency of a minimal metabolic network Several groups have recently investigated the system properties that emerge from the network organization of natural metabolisms to gain insights on the organizational and evolutionary principles of the metabolism of living organisms (Jeong et al 2000;Wagner & Fell 2001;Ma & Zeng 2003;Arita 2004;Tanaka 2005). Albeit deriving quite different conclusions, they all found that natural metabolisms can be described as networks following a power-law distribution of connectivities, i.e.…”

Section: Resultsmentioning

confidence: 99%

“…For this purpose, we used the atomic mappings of the corresponding reactions annotated in the RPAIR database (Hattori et al 2003). Finally, we automatically checked for errors in the directionality of the reaction detected by Ma & Zeng (2003) and made efforts to correct additional obvious inconsistencies. The final database comprised a total 8115 reactions.…”

Section: Methodsmentioning

confidence: 99%

Structural analyses of a hypothetical minimal metabolism

Gabaldón

Peretó

Montero

et al. 2007

Phil. Trans. R. Soc. B

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By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steadystate solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed.

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Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

Abstract: Bioinformatics Online.

Cited by 435 publications

References 24 publications

Network motif frequency vectors reveal evolving metabolic network organisation

Network motif frequency vectors reveal evolving metabolic network organisation

Extracting the hierarchical organization of complex systems

Structural analyses of a hypothetical minimal metabolism

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